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Title: Evolution of a minimal cell

Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life1,2. Here we report on how an engineered minimal cell3,4contends with the forces of evolution compared with theMycoplasma mycoidesnon-minimal cell from which it was synthetically derived. Mutation rates were the highest among all reported bacteria, but were not affected by genome minimization. Genome streamlining was costly, leading to a decrease in fitness of greater than 50%, but this deficit was regained during 2,000 generations of evolution. Despite selection acting on distinct genetic targets, increases in the maximum growth rate of the synthetic cells were comparable. Moreover, when performance was assessed by relative fitness, the minimal cell evolved 39% faster than the non-minimal cell. The only apparent constraint involved the evolution of cell size. The size of the non-minimal cell increased by 80%, whereas the minimal cell remained the same. This pattern reflected epistatic effects of mutations inftsZ, which encodes a tubulin-homologue protein that regulates cell division and morphology5,6. Our findings demonstrate that natural selection can rapidly increase the fitness of one of the simplest autonomously growing organisms. Understanding how species with small genomes overcome evolutionary challenges provides critical insights into the persistence of host-associated endosymbionts, the stability of streamlined chassis for biotechnology and the targeted refinement of synthetically engineered cells2,7–9.

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Award ID(s):
1840301 1818344 1840320 2221237
Author(s) / Creator(s):
; ; ; ; ; ; ; ;
Publisher / Repository:
Date Published:
Journal Name:
Page Range / eLocation ID:
122 to 127
Subject(s) / Keyword(s):
["Experimental evolution, Bacterial genes, Genome evolution, Synthetic organisms, Molecular evolution"]
Medium: X
Sponsoring Org:
National Science Foundation
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  1. Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life. Here, we report on how a synthetically constructed minimal cell contends with the forces of evolution compared to a non-minimized cell from which it was derived. Genome streamlining was costly, but 80% of fitness was regained in 2000 generations. Although selection acted upon divergent sets of mutations, the rates of adaptation in the minimal and non-minimal cell were equivalent. The only apparent constraint of minimization involved epistatic interactions that inhibited the evolution of cell size. Together, our findings demonstrate the power of natural selection to rapidly optimize fitness in the simplest autonomous organism, with implications for the evolution of cellular complexity. 
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  2. Abstract

    A barrier to cost‐efficient biomanufacturing is the instability of engineered genetic elements, such as plasmids. Instability can also manifest at the whole‐genome level, when fungal dikaryons revert to parental species due to nuclear segregation during cell division. Here, we show that by encapsulatingSaccharomyces cerevisiaePichia stipitisdikaryons in an alginate matrix, we can limit cell division and preserve their expanded metabolic capabilities. As a proxy to cellulosic ethanol production, we tested the capacity of such cells to carry out ethanologenic fermentation of glucose and xylose, examining substrate use, ploidy, and cell viability in relation to planktonic fusants, as well as in relation to planktonic and encapsulated cell cultures consisting of mixtures of these species. Glucose and xylose consumption and ethanol production by encapsulated dikaryons were greater than planktonic controls. Simultaneous co‐fermentation did not occur; rather the order and kinetics of glucose and xylose catabolism by encapsulated dikaryons were similar to cultures where the two species were encapsulated together. Over repeated cycles of fed‐batch culture, encapsulatedS. cerevisiae‐P. stipitisfusants exhibited a dramatic increase in genomic stability, relative to planktonic fusants. Encapsulation also increased the stability of antibiotic‐resistance plasmids used to mark each species and preserved a fixed ratio ofS. cerevisiaetoP. stipitiscells in mixed cultures. Our data demonstrate how encapsulating cells in an extracellular matrix restricts cell division and, thereby, preserves the stability and biological activity of entities ranging from genomes to plasmids to mixed populations, each of which can be essential to cost‐efficient biomanufacturing.

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  3. Premise

    Male gametophytes of most seed plants deliver sperm to eggs via a pollen tube. Pollen tube growth rates (PTGRs) of angiosperms are exceptionally rapid, a pattern attributed to more effective haploid selection under stronger pollen competition. Paradoxically, whole genome duplication (WGD) has been common in angiosperms but rare in gymnosperms. Pollen tube polyploidy should initially acceleratePTGRbecause increased heterozygosity and gene dosage should increase metabolic rates. However, polyploidy should also independently increase tube cell size, causing more work which should decelerate growth. We asked how genome size changes have affected the evolution of seed plantPTGRs.


    We assembled a phylogenetic tree of 451 species with knownPTGRs. We then used comparative phylogenetic methods to detect effects of neo‐polyploidy (within‐genus origins),DNAcontent, andWGDhistory onPTGR, and correlated evolution ofPTGRandDNAcontent.


    Gymnosperms had significantly higherDNAcontent and slowerPTGRoptima than angiosperms, and theirPTGRandDNAcontent were negatively correlated. For angiosperms, 89% of model weight favored Ornstein‐Uhlenbeck models with a fasterPTGRoptimum for neo‐polyploids, whereasPTGRandDNAcontent were not correlated. For within‐genus and intraspecific‐cytotype pairs,PTGRs of neo‐polyploids < paleo‐polyploids.


    Genome size increases should negatively affectPTGRwhen genetic consequences ofWGDs are minimized, as found in intra‐specific autopolyploids (low heterosis) and gymnosperms (fewWGDs). But in angiosperms, the higherPTGRoptimum of neo‐polyploids and non‐negativePTGRDNAcontent correlation suggest that recurrentWGDs have caused substantialPTGRevolution in a non‐haploid state.

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  4. Ever-increasing demands for energy, particularly being environmentally friendly have promoted the transition from fossil fuels to renewable energy.1Lithium-ion batteries (LIBs), arguably the most well-studied energy storage system, have dominated the energy market since their advent in the 1990s.2However, challenging issues regarding safety, supply of lithium, and high price of lithium resources limit the further advancement of LIBs for large-scale energy storage applications.3Therefore, attention is being concentrated on an alternative electrochemical energy storage device that features high safety, low cost, and long cycle life. Rechargeable aqueous zinc-ion batteries (ZIBs) is considered one of the most promising alternative energy storage systems due to the high theoretical energy and power densities where the multiple electrons (Zn2+) . In addition, aqueous ZIBs are safer due to non-flammable electrolyte (e.g., typically aqueous solution) and can be manufactured since they can be assembled in ambient air conditions.4As an essential component in aqueous Zn-based batteries, the Zn metal anode generally suffers from the growth of dendrites, which would affect battery performance in several ways. Second, the led by the loose structure of Zn dendrite may reduce the coulombic efficiency and shorten the battery lifespan.5

    Several approaches were suggested to improve the electrochemical stability of ZIBs, such as implementing an interfacial buffer layer that separates the active Zn from the bulk electrolyte.6However, the and thick thickness of the conventional Zn metal foils remain a critical challenge in this field, which may diminish the energy density of the battery drastically. According to a theretical calculation, the thickness of a Zn metal anode with an areal capacity of 1 mAh cm-2is about 1.7 μm. However, existing extrusion-based fabrication technologies are not capable of downscaling the thickness Zn metal foils below 20 μm.

    Herein, we demonstrate a thickness controllable coating approach to fabricate an ultrathin Zn metal anode as well as a thin dielectric oxide separator. First, a 1.7 μm Zn layer was uniformly thermally evaporated onto a Cu foil. Then, Al2O3, the separator was deposited through sputtering on the Zn layer to a thickness of 10 nm. The inert and high hardness Al2O3layer is expected to lower the polarization and restrain the growth of Zn dendrites. Atomic force microscopy was employed to evaluate the roughness of the surface of the deposited Zn and Al2O3/Zn anode structures. Long-term cycling stability was gauged under the symmetrical cells at 0.5 mA cm-2for 1 mAh cm-2. Then the fabricated Zn anode was paired with MnO2as a full cell for further electrochemical performance testing. To investigate the evolution of the interface between the Zn anode and the electrolyte, a home-developed in-situ optical observation battery cage was employed to record and compare the process of Zn deposition on the anodes of the Al2O3/Zn (demonstrated in this study) and the procured thick Zn anode. The surface morphology of the two Zn anodes after circulation was characterized and compared through scanning electron microscopy. The tunable ultrathin Zn metal anode with enhanced anode stability provides a pathway for future high-energy-density Zn-ion batteries.

    Obama, B., The irreversible momentum of clean energy.Science2017,355(6321), 126-129.

    Goodenough, J. B.; Park, K. S., The Li-ion rechargeable battery: a perspective.J Am Chem Soc2013,135(4), 1167-76.

    Li, C.; Xie, X.; Liang, S.; Zhou, J., Issues and Future Perspective on Zinc Metal Anode for Rechargeable Aqueous Zinc‐ion Batteries.Energy & Environmental Materials2020,3(2), 146-159.

    Jia, H.; Wang, Z.; Tawiah, B.; Wang, Y.; Chan, C.-Y.; Fei, B.; Pan, F., Recent advances in zinc anodes for high-performance aqueous Zn-ion batteries.Nano Energy2020,70.

    Yang, J.; Yin, B.; Sun, Y.; Pan, H.; Sun, W.; Jia, B.; Zhang, S.; Ma, T., Zinc Anode for Mild Aqueous Zinc-Ion Batteries: Challenges, Strategies, and Perspectives.Nanomicro Lett2022,14(1), 42.

    Yang, Q.; Li, Q.; Liu, Z.; Wang, D.; Guo, Y.; Li, X.; Tang, Y.; Li, H.; Dong, B.; Zhi, C., Dendrites in Zn-Based Batteries.Adv Mater2020,32(48), e2001854.


    This work was partially supported by the U.S. National Science Foundation (NSF) Award No. ECCS-1931088. S.L. and H.W.S. acknowledge the support from the Improvement of Measurement Standards and Technology for Mechanical Metrology (Grant No. 22011044) by KRISS.

    Figure 1


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  5. Abstract

    CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2–18-fold compared to wild-type Cas12a when using HDR donors containing mismatches with crRNA at the PAM-distal region. Finally, a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The available structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome-editing proteins.

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